Index: /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/Benchmark_2_Bathymetry.lic
===================================================================
--- /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/Benchmark_2_Bathymetry.lic	(revision 8461)
+++ /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/Benchmark_2_Bathymetry.lic	(revision 8461)
@@ -0,0 +1,18 @@
+<?xml version='1.0' encoding='iso-8859-1'?>
+<ga_license_file>
+  <metadata>
+    <author>Ole Nielsen</author>
+  </metadata>
+  
+  <datafile>
+    <filename>Benchmark_2_Bathymetry.pts</filename>
+    <checksum>204947807</checksum>
+    <publishable>Yes</publishable>
+    <accountable>Ole Nielsen</accountable>
+    <source>http://www.cee.cornell.edu/longwave</source>
+    <IP_owner>Central Research Institute for Electric Power Industry (CRIEPI) in Abiko, Japan</IP_owner>
+    <IP_info>This dataset was published as part of THE THIRD INTERNATIONAL WORKSHOP ON LONG-WAVE RUNUP MODELS held June 17-18 2004 at Wrigley Marine Science Center, Catalina Island, California. See Benchmark #2 on the website. This file has been converted from the bathymetry published on the website.
+    </IP_info>
+  </datafile>
+
+</ga_license_file>
Index: /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/Benchmark_2_input.lic
===================================================================
--- /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/Benchmark_2_input.lic	(revision 8461)
+++ /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/Benchmark_2_input.lic	(revision 8461)
@@ -0,0 +1,18 @@
+<?xml version='1.0' encoding='iso-8859-1'?>
+<ga_license_file>
+  <metadata>
+    <author>Ole Nielsen</author>
+  </metadata>
+  
+  <datafile>
+    <filename>Benchmark_2_input.txt</filename>
+    <checksum>1408559107</checksum>
+    <publishable>Yes</publishable>
+    <accountable>Ole Nielsen</accountable>
+    <source>http://www.cee.cornell.edu/longwave</source>
+    <IP_owner>Central Research Institute for Electric Power Industry (CRIEPI) in Abiko, Japan</IP_owner>
+    <IP_info>This dataset was published as part of THE THIRD INTERNATIONAL WORKSHOP ON LONG-WAVE RUNUP MODELS held June 17-18 2004 at Wrigley Marine Science Center, Catalina Island, California. See Benchmark #2 on the website.
+    </IP_info>
+  </datafile>
+
+</ga_license_file>
Index: /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/Benchmark_2_input.txt
===================================================================
--- /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/Benchmark_2_input.txt	(revision 8461)
+++ /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/Benchmark_2_input.txt	(revision 8461)
@@ -0,0 +1,452 @@
+time(s)     water surface(m)
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+2.50000E-01	2.87000E-05
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+1.93500E+01	-9.33460E-03
+1.94000E+01	-9.49450E-03
+1.94500E+01	-9.65100E-03
+1.95000E+01	-9.80400E-03
+1.95500E+01	-9.95320E-03
+1.96000E+01	-1.00984E-02
+1.96500E+01	-1.02393E-02
+1.97000E+01	-1.03753E-02
+1.97500E+01	-1.05060E-02
+1.98000E+01	-1.06310E-02
+1.98500E+01	-1.07499E-02
+1.99000E+01	-1.08621E-02
+1.99500E+01	-1.09673E-02
+2.00000E+01	-1.10650E-02
+2.00500E+01	-1.11548E-02
+2.01000E+01	-1.12362E-02
+2.01500E+01	-1.13088E-02
+2.02000E+01	-1.13718E-02
+2.02500E+01	-1.14245E-02
+2.03000E+01	-1.14658E-02
+2.03500E+01	-1.14947E-02
+2.04000E+01	-1.15097E-02
+2.04500E+01	-1.15091E-02
+2.05000E+01	-1.14911E-02
+2.05500E+01	-1.14535E-02
+2.06000E+01	-1.13941E-02
+2.06500E+01	-1.13106E-02
+2.07000E+01	-1.12004E-02
+2.07500E+01	-1.10612E-02
+2.08000E+01	-1.08907E-02
+2.08500E+01	-1.06871E-02
+2.09000E+01	-1.04486E-02
+2.09500E+01	-1.01742E-02
+2.10000E+01	-9.86310E-03
+2.10500E+01	-9.51560E-03
+2.11000E+01	-9.13240E-03
+2.11500E+01	-8.71500E-03
+2.12000E+01	-8.26570E-03
+2.12500E+01	-7.78770E-03
+2.13000E+01	-7.28470E-03
+2.13500E+01	-6.76120E-03
+2.14000E+01	-6.22220E-03
+2.14500E+01	-5.67330E-03
+2.15000E+01	-5.12000E-03
+2.15500E+01	-4.56850E-03
+2.16000E+01	-4.02450E-03
+2.16500E+01	-3.49370E-03
+2.17000E+01	-2.98140E-03
+2.17500E+01	-2.49260E-03
+2.18000E+01	-2.03140E-03
+2.18500E+01	-1.60130E-03
+2.19000E+01	-1.20500E-03
+2.19500E+01	-8.44200E-04
+2.20000E+01	-5.19800E-04
+2.20500E+01	-2.31900E-04
+2.21000E+01	2.03000E-05
+2.21500E+01	2.38400E-04
+2.22000E+01	4.24600E-04
+2.22500E+01	5.81700E-04
+2.23000E+01	7.12600E-04
+2.23500E+01	8.21000E-04
+2.24000E+01	9.10200E-04
+2.24500E+01	9.83800E-04
+2.25000E+01	1.04510E-03
Index: /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/compare_timeseries_with_measures.py
===================================================================
--- /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/compare_timeseries_with_measures.py	(revision 8461)
+++ /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/compare_timeseries_with_measures.py	(revision 8461)
@@ -0,0 +1,253 @@
+"""Verify that simulation produced by ANUGA compares to published
+validation timeseries ch5, ch7 and ch9 as well as the boundary timeseries.
+
+RMS norm is printed and plots are produced as png files.
+No plots are shown on screen.
+"""
+
+import sys
+
+import numpy as num
+from Scientific.IO.NetCDF import NetCDFFile
+
+import project
+from anuga.abstract_2d_finite_volumes.util import file_function
+from anuga.utilities.numerical_tools import\
+     ensure_numeric, cov, get_machine_precision
+from anuga.shallow_water.sww_interrogate import get_maximum_inundation_elevation
+from anuga.shallow_water.sww_interrogate import get_maximum_inundation_location
+from anuga.geometry.polygon import is_inside_polygon
+from create_okushiri import gulleys
+
+if sys.platform == 'win32':
+    # Windows has a problem when this module is run through
+    # os.system as done by validate_okushiri.
+    # See https://datamining.anu.edu.au/anuga/ticket/235
+
+    # If you want to see the plots from this validation,
+    # run this module by itself with this if clause removed.
+    plotting = False
+    
+else:
+    try:
+        from pylab import ion, hold, plot, title, legend
+        from pylab import xlabel, ylabel, savefig
+        hold(False)  # Check if this command can be issued
+    except:
+        print 'Could not import pylab'
+        plotting = False
+    else:
+        # Create plots as png files
+        plotting = True
+    
+
+#-------------------------
+# Basic data
+#-------------------------
+
+finaltime = 22.5
+timestep = 0.05
+
+gauge_locations = [[0.000, 1.696]] # Boundary gauge
+gauge_locations += [[4.521, 1.196],  [4.521, 1.696],  [4.521, 2.196]] #Ch 5-7-9
+gauge_names = ['Boundary', 'ch5', 'ch7', 'ch9']
+
+validation_data = {}
+for key in gauge_names:
+    validation_data[key] = []
+
+
+# Expected values
+expected_covariance = {'Boundary': 5.269569575007607815e-05, 
+                       'ch5': 1.166277999581819919e-04,
+                       'ch7': 1.127136457890861503e-04,
+                       'ch9': 1.250659477418482129e-04}
+
+expected_difference = {'Boundary': 8.350712673810733924e-04,
+                       'ch5': 3.405426180525532483e-03,
+                       'ch7': 2.852870417368218517e-03,
+                       'ch9': 3.248778982037564891e-03}
+
+expected_maximum = {'Boundary': 1.611749508386188523e-02,  
+                    'ch5': 3.551308418158714147e-02,
+                    'ch7': 3.858418457126511908e-02,
+                    'ch9': 4.317962986578308127e-02}
+
+expected_minimum = {'Boundary': -1.164547474575844919e-02, 
+                    'ch5': -8.664439185502026408e-03,
+                    'ch7': -2.726335488279797541e-03,
+                    'ch9': -5.977581218447349659e-03}
+
+expected_argmax = {'Boundary': 1.255000000000000071e+01, 
+                   'ch5': 1.839999999999999858e+01,
+                   'ch7': 1.700000000000000000e+01,
+                   'ch9': 1.685000000000000142e+01}
+
+expected_argmin = {'Boundary': 2.064999999999999858e+01, 
+                   'ch5': 1.459999999999999964e+01,
+                   'ch7': 1.230000000000000071e+01,
+                   'ch9': 1.315000000000000036e+01}
+
+#-------------------------
+# Read validation dataa
+#-------------------------
+
+print 'Reading', project.boundary_filename
+fid = NetCDFFile(project.boundary_filename, 'r')
+input_time = fid.variables['time'][:]
+validation_data['Boundary'] = fid.variables['stage'][:]
+
+reference_time = []
+fid = open(project.validation_filename)
+lines = fid.readlines()
+fid.close()
+
+for i, line in enumerate(lines[1:]):
+    if i == len(input_time): break
+    
+    fields = line.split()
+
+    reference_time.append(float(fields[0]))    # Record reference time
+    for j, key in enumerate(gauge_names[1:]):  # Omit boundary gauge
+        value = float(fields[1:][j])           # Omit time 
+        validation_data[key].append(value/100) # Convert cm2m
+
+
+# Checks
+assert reference_time[0] == 0.0
+assert reference_time[-1] == finaltime
+assert num.allclose(reference_time, input_time)
+
+for key in gauge_names:
+    validation_data[key] = ensure_numeric(validation_data[key])
+
+#--------------------------------------------------
+# Read and interpolate model output
+#--------------------------------------------------
+
+if len(sys.argv) > 1:
+    sww_filename = sys.argv[1]
+else:    
+    sww_filename = project.output_filename
+    
+f = file_function(sww_filename,
+                  quantities='stage',
+                  interpolation_points=gauge_locations,
+                  use_cache=True,
+                  verbose=True)
+
+
+def report_difference(name, computed_value, reference_value, rtol, atol):
+
+    if abs(reference_value) > 0:
+        msg = '%s (expected, computed):\n  (%.18e, %.18e):\n  Relative error=%.18e'\
+              %(name, reference_value, computed_value,
+                abs(reference_value-computed_value)/reference_value)
+        print msg
+        
+
+    msg = '  Absolute error=%.18e'\
+          %(abs(reference_value-computed_value))        
+    print msg
+
+    
+    #print 'Allclose:', allclose(reference_value, computed_value,
+    #                            rtol=rtol, atol=atol)
+    if plotting is False:
+        assert num.allclose(reference_value, computed_value,
+                            rtol=rtol, atol=atol), msg
+    
+
+
+#--------------------------------------------------
+# Compare model output to validation data
+#--------------------------------------------------
+
+
+#eps = get_machine_precision()
+
+# Windows tolerances
+rtol = 1.0e-2
+atol = 1.0e-3
+print 'Precisions used: rtol=%e, atol=%e' %(rtol, atol)
+
+for k, name in enumerate(gauge_names):
+
+    sqsum = 0
+    denom = 0
+    model = []
+    print 
+    print 'Validating ' + name
+    observed_timeseries = validation_data[name]
+    for i, t in enumerate(reference_time):
+        model.append(f(t, point_id=k)[0])
+
+    # Covariance measure    
+    res = cov(observed_timeseries, model)
+    report_difference('Covariance', res, expected_covariance[name], rtol, atol)
+     
+    # Difference measures    
+    res = sum(abs(observed_timeseries-model))/len(model)
+    report_difference('Accumulated difference', res,
+                      expected_difference[name], rtol, atol)    
+
+    # Extrema
+    res = max(model)
+    report_difference('Maximum', res, expected_maximum[name], rtol, atol)
+    
+    res = min(model)
+    report_difference('Minimum', res, expected_minimum[name], rtol, atol)    
+
+    # Locations of extrema
+    #i0 = argmax(observed_timeseries)
+    i1 = num.argmax(model)
+    res = reference_time[i1]
+    report_difference('Location of maximum', res, expected_argmax[name], rtol, atol)    
+    
+
+    if not name in ['ch7', 'ch9']:
+        # Minima of ch7 and ch9 are very flat and hard to pinpoint
+        i1 = num.argmin(model)
+        res = reference_time[i1]
+        report_difference('Location of minimum', res, expected_argmin[name],
+                          rtol, atol)        
+
+
+    if plotting is True:
+        #ion() # No plotting on screen
+        hold(False)
+    
+        plot(reference_time, validation_data[name], 'r-',
+             reference_time, model, 'k-')
+        title('Gauge %s' %name)
+        xlabel('time(s)')
+        ylabel('stage (m)')    
+        legend(('Observed', 'Modelled'), shadow=True, loc='upper left')
+        savefig(name, dpi = 300)        
+
+
+
+
+# Check max runup
+
+q = get_maximum_inundation_elevation(sww_filename)
+loc = get_maximum_inundation_location(sww_filename)
+
+
+print 'Max runup elevation: ', q
+print 'Max runup elevation (scaled by 400): ', q*400
+print 'Max runup location:  ', loc
+
+
+assert is_inside_polygon(loc, gulleys)
+
+# FIXME more asserts here
+
+
+
+#msg = 'We got %f, should have been %f' %(q, q_max)
+#assert allclose(q, q_max, rtol=1.0/N), msg
+##print 'loc', loc, q
+#assert allclose(-loc[0]/2, q) # From topography formula 
+
+print 'OK'
Index: /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/compare_timeseries_with_measures.stdout
===================================================================
--- /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/compare_timeseries_with_measures.stdout	(revision 8461)
+++ /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/compare_timeseries_with_measures.stdout	(revision 8461)
@@ -0,0 +1,184 @@
+Reading Benchmark_2_input.tms
+Caching: looking for cached files /home/steve/.python_cache/_file_function[-3462576297556829538]_{Result,Args,Admin}.z
+Caching: Dependencies are ['okushiri_auto_validation.sww']
+Dependencies ['okushiri_auto_validation.sww'] have changed - recomputing
++-------------------------------------------------------------
+| Fri May 18 18:02:03 2012. Evaluating function _file_function
++-------------------------------------------------------------
+
+| Argument:     'okushiri_auto_validation.sww'
+| Keyword Args: {'time_limit': None, 'interpolation_points': [[0.0, 1.696], [4.521, 1.196], [4.521, 1.696], [4.521, 2.196]], 'verbose': True, 'domain_starttime': None, 'boundary_polygon': None, 'quantities': 'stage', 'time_thinning': 1, 'output_centroids': False}
+| Reason:       Dependencies have changed
++-------------------------------------------------------------
+
+Reading okushiri_auto_validation.sww
+File_function data obtained from: okushiri_auto_validation.sww
+  References:
+    Lower left corner: [0.000000, 0.000000]
+    Start time:   0.000000
+Calling interpolation function
+Interpolation_function: input checks
+Interpolation_function: thinning by 1
+Interpolation_function: precomputing
+Build interpolator
+Building interpolation matrix from source mesh (20802 vertices, 41502 triangles)
+FitInterpolate: Building mesh
+FitInterpolate: Building quad tree
+Interpolating (4 interpolation points, 451 timesteps).
+
+  time step 0 of 451
+    quantity stage, size=20802
+  time step 46 of 451
+    quantity stage, size=20802
+  time step 92 of 451
+    quantity stage, size=20802
+  time step 138 of 451
+    quantity stage, size=20802
+  time step 184 of 451
+    quantity stage, size=20802
+  time step 230 of 451
+    quantity stage, size=20802
+  time step 276 of 451
+    quantity stage, size=20802
+  time step 322 of 451
+    quantity stage, size=20802
+  time step 368 of 451
+    quantity stage, size=20802
+  time step 414 of 451
+    quantity stage, size=20802
+------------------------------------------------
+Interpolation_function (spatio-temporal) statistics:
+  Extent:
+    x in [0.000000, 5.448000], len(x) == 20802
+    y in [0.000000, 3.402000], len(y) == 20802
+    t in [0.000000, 22.500000], len(t) == 451
+  Quantities:
+    stage in [-0.024492, 0.126906]
+  Interpolation points (xi, eta): number of points == 4
+    xi in [0.000000, 4.521000]
+    eta in [1.196000, 2.196000]
+  Interpolated quantities (over all timesteps):
+    stage at interpolation points in [-0.012413, 0.044416]
+------------------------------------------------
+
++-------------------------------------------------------
+| Fri May 18 18:02:32 2012. Caching statistics (storing)
++-------------------------------------------------------
+
+| Function:     _file_function
+| Argument:     'okushiri_auto_validation.sww'
+| Keyword Args: {'time_limit': None, 'interpolation_points': [[0.0, 1.696], [4.521, 1.196], [4.521, 1.696], [4.521, 2.196]], 'verbose': True, 'domain_starttime': None, 'boundary_polygon': None, 'quantities': 'stage', 'time_thinning': 1, 'output_centroids': False}
+| Reason:       Dependencies have changed
+| CPU time:     29.33 seconds
+| Loading time: 0.0 seconds (estimated)
+|
+| Caching dir:  /home/steve/.python_cache/
+| Result file:  _file_function[-3462576297556829538]_Result(351649 bytes)
+| Args file:    _file_function[-3462576297556829538]_Args(305 bytes)
+| Admin file:   _file_function[-3462576297556829538]_Admin(610 bytes)
+|
+| Dependencies:  
+| okushiri_auto_validation.sww: Fri May 18 18:02:02 2012 113333304 bytes
++-------------------------------------------------------
+
+Precisions used: rtol=1.000000e-02, atol=1.000000e-03
+
+Validating Boundary
+Covariance (expected, computed):
+  (5.269569575007607815e-05, 5.590176304163566002e-05):
+  Relative error=6.084116066642792503e-02
+  Absolute error=3.206067291559581869e-06
+Accumulated difference (expected, computed):
+  (8.350712673810733924e-04, 7.653472646024681806e-04):
+  Relative error=8.349467345137095986e-02
+  Absolute error=6.972400277860521176e-05
+Maximum (expected, computed):
+  (1.611749508386188523e-02, 1.692166168017697134e-02):
+  Relative error=4.989401840241797226e-02
+  Absolute error=8.041665963150861074e-04
+Minimum (expected, computed):
+  (-1.164547474575844919e-02, -1.241294411712453270e-02):
+  Relative error=-6.590279813586935598e-02
+  Absolute error=7.674693713660835082e-04
+Location of maximum (expected, computed):
+  (1.255000000000000071e+01, 1.250000000000000000e+01):
+  Relative error=3.984063745019976628e-03
+  Absolute error=5.000000000000071054e-02
+Location of minimum (expected, computed):
+  (2.064999999999999858e+01, 2.060000000000000142e+01):
+  Relative error=2.421307506053131404e-03
+  Absolute error=4.999999999999715783e-02
+
+Validating ch5
+Covariance (expected, computed):
+  (1.166277999581819919e-04, 1.207707263025518984e-04):
+  Relative error=3.552263136109394537e-02
+  Absolute error=4.142926344369906515e-06
+Accumulated difference (expected, computed):
+  (3.405426180525532483e-03, 3.426510366819313872e-03):
+  Relative error=6.191350267509728757e-03
+  Absolute error=2.108418629378138939e-05
+Maximum (expected, computed):
+  (3.551308418158714147e-02, 3.622844205730523653e-02):
+  Relative error=2.014350181640924692e-02
+  Absolute error=7.153578757180950598e-04
+Minimum (expected, computed):
+  (-8.664439185502026408e-03, -8.566545557533238389e-03):
+  Relative error=-1.129832247337955731e-02
+  Absolute error=9.789362796878801898e-05
+Location of maximum (expected, computed):
+  (1.839999999999999858e+01, 1.835000000000000142e+01):
+  Relative error=2.717391304347671621e-03
+  Absolute error=4.999999999999715783e-02
+Location of minimum (expected, computed):
+  (1.459999999999999964e+01, 1.455000000000000071e+01):
+  Relative error=3.424657534246502294e-03
+  Absolute error=4.999999999999893419e-02
+
+Validating ch7
+Covariance (expected, computed):
+  (1.127136457890861503e-04, 1.168179794364621808e-04):
+  Relative error=3.641381324011298826e-02
+  Absolute error=4.104333647376030543e-06
+Accumulated difference (expected, computed):
+  (2.852870417368218517e-03, 2.868605366831458638e-03):
+  Relative error=5.515479906639313319e-03
+  Absolute error=1.573494946324012142e-05
+Maximum (expected, computed):
+  (3.858418457126511908e-02, 4.074672048782244926e-02):
+  Relative error=5.604721054978158146e-02
+  Absolute error=2.162535916557330185e-03
+Minimum (expected, computed):
+  (-2.726335488279797541e-03, -2.772579138047224535e-03):
+  Relative error=-1.696183392184238622e-02
+  Absolute error=4.624364976742699473e-05
+Location of maximum (expected, computed):
+  (1.700000000000000000e+01, 1.694999999999999929e+01):
+  Relative error=2.941176470588276887e-03
+  Absolute error=5.000000000000071054e-02
+
+Validating ch9
+Covariance (expected, computed):
+  (1.250659477418482129e-04, 1.278530003035106182e-04):
+  Relative error=2.228466350740995403e-02
+  Absolute error=2.787052561662405319e-06
+Accumulated difference (expected, computed):
+  (3.248778982037564891e-03, 3.415891793780166056e-03):
+  Relative error=5.143865208023217644e-02
+  Absolute error=1.671128117426011646e-04
+Maximum (expected, computed):
+  (4.317962986578308127e-02, 4.441624373170362933e-02):
+  Relative error=2.863882506089938593e-02
+  Absolute error=1.236613865920548061e-03
+Minimum (expected, computed):
+  (-5.977581218447349659e-03, -5.963913514762151681e-03):
+  Relative error=-2.286494015843435531e-03
+  Absolute error=1.366770368519797801e-05
+Location of maximum (expected, computed):
+  (1.685000000000000142e+01, 1.685000000000000142e+01):
+  Relative error=0.000000000000000000e+00
+  Absolute error=0.000000000000000000e+00
+Max runup elevation:  0.0936680808663
+Max runup elevation (scaled by 400):  37.4672323465
+Max runup location:   [5.1611314, 1.8888974]
+OK
Index: /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/create_okushiri.py
===================================================================
--- /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/create_okushiri.py	(revision 8461)
+++ /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/create_okushiri.py	(revision 8461)
@@ -0,0 +1,171 @@
+"""Create mesh and time boundary for the Okushiri island validation
+"""
+
+
+import numpy as num
+
+from anuga.pmesh.mesh import *
+from anuga.pmesh.mesh_interface import create_mesh_from_regions
+from anuga.coordinate_transforms.geo_reference import Geo_reference
+from anuga.geospatial_data import Geospatial_data
+from anuga.config import netcdf_float
+
+import project
+
+
+
+
+#--------------------------------------------------------------------------
+# Create the triangular mesh based on overall clipping polygon with a
+# tagged
+# boundary and interior regions defined in project.py along with
+# resolutions (maximal area of per triangle) for each polygon
+#--------------------------------------------------------------------------
+
+
+base_resolution = 1 # Use this to coarsen or refine entire mesh. 
+
+# Basic geometry and bounding polygon
+xleft   = 0
+xright  = 5.448
+ybottom = 0
+ytop    = 3.402
+
+point_sw = [xleft, ybottom]
+point_se = [xright, ybottom]
+point_nw = [xleft, ytop]    
+point_ne = [xright, ytop]
+
+bounding_polygon = [point_se,
+                    point_ne,
+                    point_nw,
+                    point_sw]
+
+
+# Localised refined area for gulleys
+xl = 4.8
+xr = 5.3
+yb = 1.6
+yt = 2.3
+p0 = [xl, yb]
+p1 = [xr, yb]
+p2 = [xr, yt]
+p3 = [xl, yt]
+
+gulleys = [p0, p1, p2, p3]
+
+
+
+# Island area and drawdown region
+island_0 = [xleft + 2*(xright-xleft)/3+1.2, ytop-0.5]
+island_1 = [xleft + 2*(xright-xleft)/3+0.5, ybottom + 2*(ytop-ybottom)/3]
+island_2 = [xleft + (xright-xleft)/2+0.4, ybottom + 2*(ytop-ybottom)/3-0.3]
+island_3 = [xleft + (xright-xleft)/2+0.4, ybottom + (ytop-ybottom)/3+0.3]
+island_4 = [xleft + 2*(xright-xleft)/3+0.4, ybottom + (ytop-ybottom)/3-0.3]
+island_5 = [xleft + 2*(xright-xleft)/3+1.2, ybottom+0.8]
+island_6 = [xl-.01, yb]  # Keep right edge just off the gulleys
+island_7 = [xl-.01, yt]
+
+island = [island_0, island_1, island_2,
+          island_3, island_4, island_5,
+          island_6, island_7]
+
+
+
+# Region spanning half right hand side of domain just inside boundary
+rhs_nw = [xleft + (xright-xleft)/3+1, ytop-1.4]
+rhs_sw = [xleft + (xright-xleft)/3+1, ybottom+0.5]
+rhs_se = [xright-0.1, ybottom+0.2]
+rhs_ne = [xright-0.1, ytop-0.2]        
+
+rhs_region = [rhs_nw, rhs_ne, rhs_se, rhs_sw]
+
+
+# Interior regions and creation of mesh
+interior_regions = [[rhs_region, 0.0005],
+                    [island, 0.0003*base_resolution],
+                    [gulleys, 0.00003*base_resolution]]    
+
+
+
+
+def prepare_timeboundary(filename):
+    """Convert benchmark 2 time series to NetCDF tms file.
+    This is a 'throw-away' code taylor made for files like
+    'Benchmark_2_input.txt' from the LWRU2 benchmark
+    """
+
+    from Scientific.IO.NetCDF import NetCDFFile
+
+    print 'Creating', filename
+
+    # Read the ascii (.txt) version of this file
+    fid = open(filename[:-4] + '.txt')
+
+    # Skip first line
+    line = fid.readline()
+
+    # Read remaining lines
+    lines = fid.readlines()
+    fid.close()
+
+
+    N = len(lines)
+    T = num.zeros(N, num.float)  #Time
+    Q = num.zeros(N, num.float)  #Values
+
+    for i, line in enumerate(lines):
+        fields = line.split()
+
+        T[i] = float(fields[0])
+        Q[i] = float(fields[1])
+
+
+    # Create tms NetCDF file
+
+    fid = NetCDFFile(filename, 'w')
+    fid.institution = 'Geoscience Australia'
+    fid.description = 'Input wave for Benchmark 2'
+    fid.starttime = 0.0
+    fid.createDimension('number_of_timesteps', len(T))
+    fid.createVariable('time', netcdf_float, ('number_of_timesteps',))
+    fid.variables['time'][:] = T
+
+    fid.createVariable('stage', netcdf_float, ('number_of_timesteps',))
+    fid.variables['stage'][:] = Q[:]
+
+    fid.createVariable('xmomentum', netcdf_float, ('number_of_timesteps',))
+    fid.variables['xmomentum'][:] = 0.0
+
+    fid.createVariable('ymomentum', netcdf_float, ('number_of_timesteps',))
+    fid.variables['ymomentum'][:] = 0.0
+
+    fid.close()
+
+
+def create_mesh(elevation_in_mesh=False):
+    # Prepare time boundary
+    prepare_timeboundary(project.boundary_filename)
+
+
+
+    meshname = project.mesh_filename + '.msh'
+    m = create_mesh_from_regions(bounding_polygon,
+                                 boundary_tags={'wall': [0, 1, 3],
+                                                'wave': [2]},     
+                                 maximum_triangle_area=0.1*base_resolution,
+                                 interior_regions=interior_regions,
+                                 filename=project.mesh_filename,
+                                 use_cache=False,
+                                 verbose=True)
+    
+    if elevation_in_mesh is True:
+        fit_to_mesh_file(project.mesh_filename, project.bathymetry_filename,
+                         project.mesh_filename)
+
+
+#-------------------------------------------------------------
+if __name__ == "__main__":
+    create_mesh()
+
+
Index: /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/create_okushiri.stdout
===================================================================
--- /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/create_okushiri.stdout	(revision 8461)
+++ /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/create_okushiri.stdout	(revision 8461)
@@ -0,0 +1,26 @@
+Creating Benchmark_2_input.tms
+Generating mesh to file 'Benchmark_2.msh'
+Constructing Delaunay triangulation by divide-and-conquer method.
+Recovering segments in Delaunay triangulation.
+Removing unwanted triangles.
+Spreading regional attributes and area constraints.
+Adding Steiner points to enforce quality.
+
+Writing vertices.
+Writing triangles.
+Writing segments.
+Writing neighbors.
+
+Statistics:
+
+  Input vertices: 20
+  Input segments: 20
+  Input holes: 0
+
+  Mesh vertices: 20802
+  Mesh triangles: 41502
+  Mesh edges: 62303
+  Mesh exterior boundary edges: 100
+  Mesh interior boundary edges: 972
+  Mesh subsegments (constrained edges): 1072
+
Index: /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/loading_pts_test.py
===================================================================
--- /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/loading_pts_test.py	(revision 8461)
+++ /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/loading_pts_test.py	(revision 8461)
@@ -0,0 +1,66 @@
+"""Validation of the AnuGA implementation of the shallow water wave equation.
+
+This script sets up Okushiri Island benchmark as published at the
+
+THE THIRD INTERNATIONAL WORKSHOP ON LONG-WAVE RUNUP MODELS
+June 17-18 2004
+Wrigley Marine Science Center
+Catalina Island, California
+http://www.cee.cornell.edu/longwave/
+
+
+The validation data was downloaded and made available in this directory
+for convenience but the original data is available at
+http://www.cee.cornell.edu/longwave/index.cfm?page=benchmark&problem=2
+where a detailed description of the problem is also available.
+
+
+Run create_okushiri.py to process the boundary condition and build a the
+mesh before running this script.
+
+"""
+
+# Module imports
+from anuga.shallow_water import Domain
+from anuga.shallow_water import Reflective_boundary
+from anuga.shallow_water import Transmissive_Momentum_Set_Stage_boundary
+from anuga.abstract_2d_finite_volumes.util import file_function
+
+from anuga_parallel.parallel_api import myid, numprocs, distribute
+
+import project
+
+
+#-------------------------
+# Create Domain from mesh
+#-------------------------
+domain = Domain(project.mesh_filename, use_cache=True, verbose=True)
+print domain.statistics()
+
+
+#-------------------------
+# Initial Conditions
+#-------------------------
+domain.set_quantity('friction', 0.0)
+domain.set_quantity('stage', 0.0)
+
+import time
+t0 = time.time()
+bathymetry_filename=project.bathymetry_filename
+bathymetry_filename='Benchmark_2_Bathymetry_very_thin.pts'
+print 'Starting domain.set_quantity.  Loading ', bathymetry_filename
+s = "domain.set_quantity('elevation',filename=bathymetry_filename,alpha=0.02,verbose=True,use_cache=True)"
+
+
+import profile, pstats
+FN = 'profile.dat'
+
+profile.run(s, FN)
+
+print 'Set_quantity elevation took %.2f seconds' %(time.time()-t0)
+
+S = pstats.Stats(FN)
+#S.sort_stats('time').print_stats(20)
+s = S.sort_stats('cumulative').print_stats(60)
+
+#print s
Index: /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/output_ch5-7-9.lic
===================================================================
--- /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/output_ch5-7-9.lic	(revision 8461)
+++ /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/output_ch5-7-9.lic	(revision 8461)
@@ -0,0 +1,18 @@
+<?xml version='1.0' encoding='iso-8859-1'?>
+<ga_license_file>
+  <metadata>
+    <author>Ole Nielsen</author>
+  </metadata>
+  
+  <datafile>
+    <filename>output_ch5-7-9.txt</filename>
+    <checksum>3250363193</checksum>
+    <publishable>Yes</publishable>
+    <accountable>Ole Nielsen</accountable>
+    <source>http://www.cee.cornell.edu/longwave</source>
+    <IP_owner>Central Research Institute for Electric Power Industry (CRIEPI) in Abiko, Japan</IP_owner>
+    <IP_info>This dataset was derived from the Excel file output_ch5-7-9.xls available on the longwave web site and stored as TAB separated ascii text. 
+    </IP_info>
+  </datafile>  
+
+</ga_license_file>
Index: /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/output_ch5-7-9.txt
===================================================================
--- /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/output_ch5-7-9.txt	(revision 8461)
+++ /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/output_ch5-7-9.txt	(revision 8461)
@@ -0,0 +1,3993 @@
+time	ch5(cm)	ch7(cm)	ch9(cm)
+0	0.234	-0.115	0.045
+0.05	0.234	0.015	0.065
+0.1	0.234	0.045	0.065
+0.15	0.234	0.045	0.085
+0.2	0.234	0.055	0.105
+0.25	0.234	0.055	0.105
+0.3	0.234	0.065	0.105
+0.35	0.234	0.065	0.105
+0.4	0.234	0.075	0.105
+0.45	0.234	0.065	0.105
+0.5	0.234	0.055	0.115
+0.55	0.234	0.065	0.115
+0.6	0.234	0.065	0.115
+0.65	0.244	0.075	0.115
+0.7	0.234	0.075	0.115
+0.75	0.244	0.075	0.115
+0.8	0.234	0.075	0.115
+0.85	0.234	0.065	0.115
+0.9	0.234	0.075	0.115
+0.95	0.244	0.065	0.125
+1	0.234	0.065	0.125
+1.05	0.244	0.075	0.135
+1.1	0.234	0.075	0.145
+1.15	0.244	0.065	0.145
+1.2	0.244	0.075	0.145
+1.25	0.244	0.075	0.135
+1.3	0.244	0.075	0.145
+1.35	0.244	0.075	0.145
+1.4	0.254	0.075	0.145
+1.45	0.254	0.075	0.145
+1.5	0.254	0.075	0.145
+1.55	0.254	0.075	0.145
+1.6	0.254	0.075	0.145
+1.65	0.254	0.075	0.145
+1.7	0.254	0.075	0.145
+1.75	0.264	0.075	0.145
+1.8	0.264	0.075	0.145
+1.85	0.274	0.075	0.145
+1.9	0.264	0.085	0.145
+1.95	0.264	0.075	0.155
+2	0.264	0.045	0.155
+2.05	0.264	0.075	0.145
+2.1	0.274	0.065	0.155
+2.15	0.274	0.075	0.155
+2.2	0.284	0.075	0.155
+2.25	0.284	0.075	0.155
+2.3	0.294	0.075	0.155
+2.35	0.304	0.085	0.155
+2.4	0.294	0.095	0.155
+2.45	0.304	0.105	0.165
+2.5	0.304	0.105	0.165
+2.55	0.314	0.115	0.165
+2.6	0.314	0.095	0.175
+2.65	0.324	0.135	0.175
+2.7	0.324	0.175	0.175
+2.75	0.324	0.205	0.185
+2.8	0.324	0.235	0.185
+2.85	0.334	0.305	0.175
+2.9	0.374	0.325	0.175
+2.95	0.394	0.335	0.175
+3	0.404	0.335	0.165
+3.05	0.424	0.335	0.165
+3.1	0.444	0.335	0.175
+3.15	0.444	0.335	0.175
+3.2	0.434	0.335	0.165
+3.25	0.434	0.345	0.175
+3.3	0.424	0.335	0.175
+3.35	0.424	0.345	0.175
+3.4	0.424	0.335	0.175
+3.45	0.424	0.355	0.185
+3.5	0.424	0.345	0.195
+3.55	0.424	0.355	0.225
+3.6	0.424	0.355	0.255
+3.65	0.434	0.355	0.265
+3.7	0.444	0.355	0.285
+3.75	0.454	0.355	0.285
+3.8	0.474	0.365	0.285
+3.85	0.484	0.365	0.295
+3.9	0.484	0.365	0.295
+3.95	0.494	0.365	0.295
+4	0.494	0.355	0.295
+4.05	0.494	0.355	0.295
+4.1	0.494	0.355	0.295
+4.15	0.494	0.355	0.305
+4.2	0.484	0.365	0.305
+4.25	0.494	0.355	0.305
+4.3	0.494	0.365	0.305
+4.35	0.504	0.355	0.315
+4.4	0.494	0.365	0.315
+4.45	0.504	0.365	0.335
+4.5	0.504	0.375	0.355
+4.55	0.504	0.365	0.375
+4.6	0.504	0.375	0.375
+4.65	0.514	0.385	0.375
+4.7	0.514	0.395	0.375
+4.75	0.514	0.415	0.365
+4.8	0.514	0.425	0.355
+4.85	0.514	0.455	0.355
+4.9	0.514	0.455	0.355
+4.95	0.514	0.465	0.355
+5	0.514	0.465	0.355
+5.05	0.514	0.465	0.355
+5.1	0.514	0.475	0.355
+5.15	0.514	0.485	0.365
+5.2	0.504	0.495	0.375
+5.25	0.504	0.495	0.385
+5.3	0.504	0.495	0.385
+5.35	0.494	0.495	0.385
+5.4	0.484	0.495	0.385
+5.45	0.484	0.495	0.385
+5.5	0.484	0.495	0.385
+5.55	0.484	0.505	0.385
+5.6	0.474	0.505	0.395
+5.65	0.474	0.495	0.385
+5.7	0.464	0.495	0.395
+5.75	0.464	0.505	0.385
+5.8	0.454	0.495	0.405
+5.85	0.454	0.495	0.395
+5.9	0.444	0.495	0.395
+5.95	0.434	0.485	0.395
+6	0.434	0.475	0.395
+6.05	0.434	0.465	0.405
+6.1	0.424	0.455	0.405
+6.15	0.424	0.455	0.405
+6.2	0.424	0.445	0.405
+6.25	0.424	0.435	0.405
+6.3	0.424	0.435	0.395
+6.35	0.424	0.425	0.395
+6.4	0.414	0.425	0.395
+6.45	0.424	0.425	0.395
+6.5	0.424	0.415	0.385
+6.55	0.424	0.405	0.385
+6.6	0.424	0.405	0.385
+6.65	0.424	0.395	0.375
+6.7	0.424	0.385	0.375
+6.75	0.424	0.375	0.375
+6.8	0.414	0.395	0.375
+6.85	0.414	0.365	0.375
+6.9	0.404	0.345	0.375
+6.95	0.404	0.335	0.365
+7	0.404	0.305	0.365
+7.05	0.404	0.285	0.365
+7.1	0.404	0.275	0.365
+7.15	0.424	0.265	0.365
+7.2	0.424	0.265	0.365
+7.25	0.424	0.275	0.365
+7.3	0.424	0.285	0.355
+7.35	0.434	0.265	0.355
+7.4	0.434	0.275	0.355
+7.45	0.434	0.275	0.355
+7.5	0.424	0.275	0.355
+7.55	0.414	0.275	0.345
+7.6	0.404	0.295	0.345
+7.65	0.394	0.325	0.345
+7.7	0.384	0.345	0.345
+7.75	0.384	0.355	0.355
+7.8	0.374	0.365	0.345
+7.85	0.374	0.375	0.345
+7.9	0.364	0.375	0.335
+7.95	0.374	0.365	0.325
+8	0.364	0.375	0.305
+8.05	0.364	0.365	0.295
+8.1	0.364	0.365	0.295
+8.15	0.354	0.355	0.285
+8.2	0.354	0.355	0.265
+8.25	0.354	0.365	0.255
+8.3	0.354	0.375	0.225
+8.35	0.354	0.365	0.225
+8.4	0.354	0.365	0.215
+8.45	0.354	0.355	0.215
+8.5	0.344	0.355	0.215
+8.55	0.354	0.355	0.215
+8.6	0.334	0.365	0.205
+8.65	0.334	0.345	0.205
+8.7	0.324	0.325	0.205
+8.75	0.304	0.285	0.195
+8.8	0.284	0.285	0.195
+8.85	0.284	0.265	0.185
+8.9	0.274	0.265	0.185
+8.95	0.274	0.275	0.175
+9	0.274	0.265	0.175
+9.05	0.274	0.265	0.175
+9.1	0.264	0.265	0.175
+9.15	0.264	0.265	0.165
+9.2	0.254	0.255	0.165
+9.25	0.264	0.255	0.165
+9.3	0.254	0.245	0.155
+9.35	0.254	0.225	0.155
+9.4	0.254	0.215	0.155
+9.45	0.254	0.185	0.145
+9.5	0.204	0.145	0.155
+9.55	0.184	0.115	0.145
+9.6	0.164	0.095	0.145
+9.65	0.154	0.075	0.145
+9.7	0.144	0.065	0.145
+9.75	0.134	0.055	0.145
+9.8	0.134	0.015	0.145
+9.85	0.124	0.025	0.135
+9.9	0.114	0.015	0.135
+9.95	0.084	0.005	0.135
+10	-0.066	-0.015	0.125
+10.05	-0.116	-0.035	0.125
+10.1	-0.156	-0.045	0.125
+10.15	-0.166	-0.055	0.115
+10.2	-0.196	-0.075	0.115
+10.25	-0.216	-0.125	0.115
+10.3	-0.236	-0.155	0.115
+10.35	-0.246	-0.175	0.115
+10.4	-0.266	-0.185	0.115
+10.45	-0.266	-0.185	0.125
+10.5	-0.286	-0.185	0.115
+10.55	-0.286	-0.195	0.125
+10.6	-0.296	-0.205	0.125
+10.65	-0.306	-0.195	0.125
+10.7	-0.336	-0.205	0.115
+10.75	-0.356	-0.205	0.115
+10.8	-0.386	-0.215	0.115
+10.85	-0.386	-0.215	0.115
+10.9	-0.406	-0.225	0.115
+10.95	-0.416	-0.235	0.095
+11	-0.436	-0.235	0.085
+11.05	-0.446	-0.225	0.075
+11.1	-0.456	-0.235	0.065
+11.15	-0.466	-0.245	0.045
+11.2	-0.486	-0.245	0.035
+11.25	-0.486	-0.245	0.035
+11.3	-0.486	-0.245	0.025
+11.35	-0.486	-0.265	0.025
+11.4	-0.496	-0.245	0.015
+11.45	-0.496	-0.265	0.015
+11.5	-0.516	-0.245	0.005
+11.55	-0.516	-0.265	0.005
+11.6	-0.516	-0.265	0.005
+11.65	-0.516	-0.275	-0.005
+11.7	-0.536	-0.285	-0.015
+11.75	-0.546	-0.285	-0.025
+11.8	-0.556	-0.285	-0.025
+11.85	-0.566	-0.295	-0.045
+11.9	-0.586	-0.295	-0.055
+11.95	-0.596	-0.305	-0.065
+12	-0.596	-0.325	-0.075
+12.05	-0.606	-0.345	-0.095
+12.1	-0.616	-0.345	-0.105
+12.15	-0.616	-0.355	-0.095
+12.2	-0.636	-0.375	-0.115
+12.25	-0.636	-0.375	-0.125
+12.3	-0.646	-0.385	-0.135
+12.35	-0.646	-0.395	-0.145
+12.4	-0.656	-0.405	-0.145
+12.45	-0.666	-0.415	-0.155
+12.5	-0.686	-0.435	-0.155
+12.55	-0.696	-0.435	-0.155
+12.6	-0.716	-0.435	-0.165
+12.65	-0.716	-0.435	-0.175
+12.7	-0.736	-0.445	-0.185
+12.75	-0.746	-0.445	-0.195
+12.8	-0.746	-0.455	-0.195
+12.85	-0.756	-0.445	-0.195
+12.9	-0.776	-0.465	-0.205
+12.95	-0.786	-0.465	-0.205
+13	-0.796	-0.465	-0.205
+13.05	-0.806	-0.465	-0.215
+13.1	-0.816	-0.475	-0.215
+13.15	-0.826	-0.485	-0.215
+13.2	-0.836	-0.485	-0.215
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+198.1	-0.416	-0.335	-0.495
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+198.25	-0.436	-0.375	-0.505
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+198.4	-0.466	-0.395	-0.515
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+198.5	-0.506	-0.425	-0.515
+198.55	-0.536	-0.435	-0.515
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+198.9	-0.866	-0.525	-0.525
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+199.05	-0.896	-0.555	-0.525
+199.1	-0.916	-0.565	-0.525
+199.15	-0.926	-0.565	-0.525
+199.2	-0.936	-0.595	-0.525
+199.25	-0.936	-0.605	-0.525
+199.3	-0.946	-0.625	-0.525
+199.35	-0.946	-0.635	-0.525
+199.4	-0.946	-0.635	-0.525
+199.45	-0.936	-0.635	-0.515
+199.5	-0.926	-0.655	-0.525
+199.55	-0.916	-0.675	-0.525
Index: /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/produce_results.py
===================================================================
--- /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/produce_results.py	(revision 8461)
+++ /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/produce_results.py	(revision 8461)
@@ -0,0 +1,21 @@
+#--------------------------------
+# Setup Default values for basis
+# algorithm parameters.
+#--------------------------------
+import argparse
+parser = argparse.ArgumentParser(description='produce results')
+parser.add_argument('-cfl', type=float, default=1.0,
+                   help='cfl condition')
+parser.add_argument('-alg', type=str, default = "1_5",
+                   help='flow algorithm')
+args = parser.parse_args()
+
+cfl = args.cfl
+alg = args.alg
+
+
+
+import dam_break
+import plot_results
+
+
Index: /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/project.py
===================================================================
--- /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/project.py	(revision 8461)
+++ /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/project.py	(revision 8461)
@@ -0,0 +1,22 @@
+"""Common filenames for Okushiri Island validation
+Formats are given as ANUGA native netCDF where applicable.
+
+"""
+
+# Given boundary wave
+boundary_filename = 'Benchmark_2_input.tms'
+
+# Observed timeseries
+validation_filename = 'output_ch5-7-9.txt'
+
+# Digital Elevation Model
+bathymetry_filename = 'Benchmark_2_Bathymetry.pts'
+
+# Triangular mesh
+mesh_filename = 'Benchmark_2.msh'
+
+# Model output
+output_filename = 'okushiri_auto_validation.sww'
+
+
+
Index: /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/results.tex
===================================================================
--- /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/results.tex	(revision 8461)
+++ /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/results.tex	(revision 8461)
@@ -0,0 +1,14 @@
+
+\section{Okushiri Benchmark}
+
+Will show results of the Okushiri Benchmark using \anuga{}.
+
+\subsection{Results}
+
+
+Will have a bunch of figures in particular the guage results at a number of sites. 
+
+
+
+
+\endinput
Index: /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/run_okushiri.py
===================================================================
--- /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/run_okushiri.py	(revision 8461)
+++ /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/run_okushiri.py	(revision 8461)
@@ -0,0 +1,85 @@
+"""Validation of the AnuGA implementation of the shallow water wave equation.
+
+This script sets up Okushiri Island benchmark as published at the
+
+THE THIRD INTERNATIONAL WORKSHOP ON LONG-WAVE RUNUP MODELS
+June 17-18 2004
+Wrigley Marine Science Center
+Catalina Island, California
+http://www.cee.cornell.edu/longwave/
+
+
+The validation data was downloaded and made available in this directory
+for convenience but the original data is available at
+http://www.cee.cornell.edu/longwave/index.cfm?page=benchmark&problem=2
+where a detailed description of the problem is also available.
+
+
+Run create_okushiri.py to process the boundary condition and build a the
+mesh before running this script.
+
+"""
+
+# Module imports
+import anuga
+
+import project
+
+def main(elevation_in_mesh=False):
+    #-------------------------
+    # Create Domain from mesh
+    #-------------------------
+    domain = anuga.Domain(project.mesh_filename, use_cache=False, verbose=True)
+    print domain.statistics()
+
+
+    #-------------------------
+    # Initial Conditions
+    #-------------------------
+    domain.set_quantity('friction', 0.0)
+    domain.set_quantity('stage', 0.0)
+    if elevation_in_mesh is False:
+        domain.set_quantity('elevation',
+                            filename=project.bathymetry_filename,
+                            alpha=0.02,                    
+                            verbose=True,
+                            use_cache=False)
+
+
+    #-------------------------
+    # Set simulation parameters
+    #-------------------------
+    domain.set_name(project.output_filename)  # Name of output sww file
+    domain.set_default_order(2)               # Apply second order scheme 
+    domain.set_minimum_storable_height(0.001) # Don't store w < 0.001m
+    domain.set_quantities_to_be_monitored('stage')
+
+    #-------------------------
+    # Boundary Conditions
+    #-------------------------
+
+    # Create boundary function from timeseries provided in file
+    function = anuga.file_function(project.boundary_filename,
+                             domain, verbose=True)
+
+    # Create and assign boundary objects
+    Bts = anuga.Transmissive_momentum_set_stage_boundary(domain, function)
+    Br = anuga.Reflective_boundary(domain)
+    domain.set_boundary({'wave': Bts, 'wall': Br})
+
+
+    #-------------------------
+    # Evolve through time
+    #-------------------------
+    import time
+    t0 = time.time()
+
+    for t in domain.evolve(yieldstep = 0.05, finaltime = 22.5):
+        domain.write_time()
+        print domain.quantity_statistics(precision='%.12f')
+
+    print 'That took %.2f seconds' %(time.time()-t0)
+
+#-------------------------------------------------------------
+if __name__ == "__main__":
+    main()
Index: /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/test_caching_of_set_quantity.py
===================================================================
--- /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/test_caching_of_set_quantity.py	(revision 8461)
+++ /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/test_caching_of_set_quantity.py	(revision 8461)
@@ -0,0 +1,108 @@
+"""This script tests that caching works for set_quantity using point 
+data from a file.
+First cache is cleared, then set_quantity is run twice checking that
+fitting is evaluated only first time and that the result from cache on the
+second round is correct.
+
+This script depends on  Benchmark_2.msh and Benchmark_2_Bathymetry.pts
+"""
+
+# Module imports
+from anuga.shallow_water.shallow_water_domain import Domain
+from anuga.caching import cache
+from anuga.fit_interpolate.fit import _fit_to_mesh
+import project
+import numpy as num
+import time
+
+internal_verbose = True # Verbosity used within this function
+
+filename=project.bathymetry_filename
+alpha=0.02
+from anuga.config import points_file_block_line_size as max_read_lines
+
+#-------------------------
+# Create Domain from mesh
+#-------------------------
+domain = cache(Domain, 
+               (project.mesh_filename, 
+                {'verbose': True}), 
+               verbose=False)
+
+# Clear caching of underlying function                                            
+args = (filename, )
+kwargs = {'vertex_coordinates': None,
+          'triangles': None,
+          'mesh': domain.mesh,
+          'point_attributes': None,
+          'alpha': alpha,
+          'verbose': internal_verbose,
+          'mesh_origin': None,
+          'data_origin': None,
+          'max_read_lines': max_read_lines,
+          'attribute_name': None 
+          }
+
+
+cache(_fit_to_mesh,
+      args, 
+      kwargs,
+      verbose=False,
+      dependencies=[filename],
+      clear=True)
+
+# Check that cache is empty      
+flag = cache(_fit_to_mesh,
+             args, 
+             kwargs,
+             verbose=False,
+             dependencies=[filename],
+             test=True)
+assert flag is None
+
+
+#-------------------------
+# Initial Conditions
+#-------------------------
+t0 = time.time()
+domain.set_quantity('elevation',
+                    filename=filename,
+                    alpha=0.02,                    
+                    verbose=internal_verbose,
+                    use_cache=True)
+compute_time = time.time()-t0
+                    
+ref = domain.get_quantity('elevation').get_values()                    
+
+# Check that cache is now present (and correct)
+flag = cache(_fit_to_mesh,
+             args, 
+             kwargs,
+             verbose=False,
+             dependencies=[filename],
+             test=True)
+             
+assert flag is not None
+res = domain.get_quantity('elevation').get_values()
+assert num.allclose(res, ref)
+
+# Now check this using the high level call
+print 'Try to read in via cache'
+t0 = time.time()
+domain.set_quantity('elevation',
+                    filename=filename,
+                    alpha=0.02,                    
+                    verbose=internal_verbose,
+                    use_cache=True)
+cache_time = time.time()-t0                    
+                    
+res = domain.get_quantity('elevation').get_values() 
+assert num.allclose(res, ref)
+
+print 'cache_time', cache_time
+print 'compute_time', compute_time
+
+msg = 'Caching did not speed things up as expected'
+msg += 'Compute time = %.f, Cache time = %.f' % (compute_time,
+                                                 cache_time)
+assert cache_time < compute_time/10, msg
Index: /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/validate_okushiri.py
===================================================================
--- /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/validate_okushiri.py	(revision 8461)
+++ /trunk/anuga_core/validation_tests/Tests/Experimental/Okushiri/validate_okushiri.py	(revision 8461)
@@ -0,0 +1,87 @@
+"""Automatic verification that the ANUGA code validates against the okushiri
+dataset as expected. See anuga_validation/okushiri_2005 for more details
+"""
+
+import unittest
+import os
+
+
+class Test_Okushiri(unittest.TestCase):
+    def setUp(self):
+        
+        # Remove garbage
+        for file in os.listdir('.'):
+            if file.endswith('.stdout') or\
+                    file.endswith('.sww') or\
+                    file.endswith('.msh'):
+                os.remove(file)
+                
+                
+    def tearDown(self):
+        pass
+
+    def test_that_output_is_as_expected(self):
+        """Test that ANUGA replicates physics of the Okushiri Island
+        wave tank experiment
+        """
+        
+        #print
+        s = 'create_okushiri.py'
+        #print s
+        res = os.system('python %s > create_okushiri.stdout' %s)
+        assert res == 0
+
+        s = 'run_okushiri.py'
+        #print s        
+        res = os.system('python %s > run_okushiri.stdout' %s)        
+        assert res == 0
+        
+        
+        s = 'compare_timeseries_with_measures.py'
+        #print s
+        res = os.system('python %s > compare_timeseries_with_measures.stdout'\
+                        %s)
+        assert res == 0
+
+
+    def test_caching_of_set_quantity(self):
+        """Test that caching of set_quantity works
+        """
+        
+        s = 'create_okushiri.py'
+        res = os.system('python %s > create_okushiri_for_caching.stdout' %s)
+        assert res == 0
+
+
+        s = 'test_caching_of_set_quantity.py'
+        res = os.system('python %s > test_caching_of_set_quantity.stdout' %s)
+        assert res == 0
+
+        
+
+    def manual_test_that_output_is_as_expected(self):
+        from run_okushiri import main
+        from create_okushiri import create_mesh
+
+        # Note, this has not been tested when code is failing.
+        # Next step, use the parrameter elevation_in_mesh
+        # and only run create_okishiri once for speed.
+        
+        res = create_mesh()
+        assert res == None
+        
+        res = main()
+        assert res == None
+        
+        s = 'compare_timeseries_with_measures.py'
+        #print s
+        res = os.system('python %s > compare_timeseries_with_measures.stdout'\
+                        %s)
+        assert res == 0
+        
+
+#-------------------------------------------------------------
+if __name__ == "__main__":
+    suite = unittest.makeSuite(Test_Okushiri, 'test')
+    runner = unittest.TextTestRunner(verbosity=2)
+    runner.run(suite)
